[R] Rmpi fails to install

rose at uni-potsdam.de rose at uni-potsdam.de
Mon Mar 7 21:53:05 CET 2011


I try to install Rmpi as root with install.packages("Rmpi").
It fails with:
...
checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to accept ISO
C89... none needed
I am here /usr and it is OpenMPI
Trying to find mpi.h ...
Found in /usr/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/lib
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2
-DOPENMPI -I/usr/local/include    -fpic  -march=nocona -O2 -pipe
-fomit-frame-pointer -c RegQuery.c -o RegQuery.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2
-DOPENMPI -I/usr/local/include    -fpic  -march=nocona -O2 -pipe
-fomit-frame-pointer -c Rmpi.c -o Rmpi.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2
-DOPENMPI -I/usr/local/include    -fpic  -march=nocona -O2 -pipe
-fomit-frame-pointer -c conversion.c -o conversion.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2
-DOPENMPI -I/usr/local/include    -fpic  -march=nocona -O2 -pipe
-fomit-frame-pointer -c internal.c -o internal.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed -o
Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib -lmpi
-lutil -lpthread -L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/Rmpi/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
/usr/lib64/R/bin/exec/R: symbol lookup
error: /usr/lib64/openmpi/mca_paffinity_linux.so: undefined symbol:
mca_base_param_reg_int

The downloaded packages are in
         ?/tmp/RtmpLvvl9R/downloaded_packages?
Updating HTML index of packages in '.Library'
Warning message:
In install.packages("Rmpi") :
   installation of package 'Rmpi' had non-zero exit status

The system is a gentoo system with openmpi-1.5.1. I am thankful for any
hint.

Juergen



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